Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes

CExplicitSpecFeatures Class Reference


Detailed Description

Features that compute the Spectrum Kernel feature space explicitly.

See also:
CCommWordStringKernel

Definition at line 26 of file ExplicitSpecFeatures.h.

Inheritance diagram for CExplicitSpecFeatures:
Inheritance graph
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List of all members.

Public Member Functions

 CExplicitSpecFeatures ()
 CExplicitSpecFeatures (CStringFeatures< uint16_t > *str, bool normalize=true)
 CExplicitSpecFeatures (const CExplicitSpecFeatures &orig)
virtual ~CExplicitSpecFeatures ()
virtual CFeaturesduplicate () const
virtual int32_t get_dim_feature_space () const
virtual float64_t dot (int32_t vec_idx1, CDotFeatures *df, int32_t vec_idx2)
virtual float64_t dense_dot (int32_t vec_idx1, const float64_t *vec2, int32_t vec2_len)
virtual void add_to_dense_vec (float64_t alpha, int32_t vec_idx1, float64_t *vec2, int32_t vec2_len, bool abs_val=false)
virtual void * get_feature_iterator (int32_t vector_index)
virtual bool get_next_feature (int32_t &index, float64_t &value, void *iterator)
virtual void free_feature_iterator (void *iterator)
virtual int32_t get_nnz_features_for_vector (int32_t num)
virtual EFeatureType get_feature_type () const
virtual EFeatureClass get_feature_class () const
virtual int32_t get_num_vectors () const
virtual int32_t get_size () const
virtual const char * get_name () const
virtual float64_t dense_dot_sgvec (int32_t vec_idx1, const SGVector< float64_t > vec2)
virtual void dense_dot_range (float64_t *output, int32_t start, int32_t stop, float64_t *alphas, float64_t *vec, int32_t dim, float64_t b)
virtual void dense_dot_range_subset (int32_t *sub_index, int32_t num, float64_t *output, float64_t *alphas, float64_t *vec, int32_t dim, float64_t b)
float64_t get_combined_feature_weight ()
void set_combined_feature_weight (float64_t nw)
SGMatrix< float64_tget_computed_dot_feature_matrix ()
SGVector< float64_tget_computed_dot_feature_vector (int32_t num)
void benchmark_add_to_dense_vector (int32_t repeats=5)
void benchmark_dense_dot_range (int32_t repeats=5)
virtual SGVector< float64_tget_mean ()
virtual SGMatrix< float64_tget_cov ()
virtual int32_t add_preprocessor (CPreprocessor *p)
 set preprocessor
virtual CPreprocessordel_preprocessor (int32_t num)
 del current preprocessor
CPreprocessorget_preprocessor (int32_t num) const
 get current preprocessor
void set_preprocessed (int32_t num)
bool is_preprocessed (int32_t num) const
int32_t get_num_preprocessed () const
 get whether specified preprocessor (or all if num=1) was/were already applied
int32_t get_num_preprocessors () const
void clean_preprocessors ()
int32_t get_cache_size () const
virtual bool reshape (int32_t num_features, int32_t num_vectors)
void list_feature_obj () const
virtual void load (CFile *loader)
virtual void save (CFile *writer)
bool check_feature_compatibility (CFeatures *f) const
bool has_property (EFeatureProperty p) const
void set_property (EFeatureProperty p)
void unset_property (EFeatureProperty p)
virtual CFeaturescreate_merged_copy (CFeatures *other)
virtual void add_subset (SGVector< index_t > subset)
virtual void remove_subset ()
virtual void remove_all_subsets ()
virtual CSubsetStackget_subset_stack ()
virtual void subset_changed_post ()
virtual CFeaturescopy_subset (SGVector< index_t > indices)
virtual CSGObjectshallow_copy () const
virtual CSGObjectdeep_copy () const
virtual bool is_generic (EPrimitiveType *generic) const
template<class T >
void set_generic ()
void unset_generic ()
virtual void print_serializable (const char *prefix="")
virtual bool save_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)
DynArray< TParameter * > * load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="")
DynArray< TParameter * > * load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="")
void map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos)
void set_global_io (SGIO *io)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_global_version ()
SGStringList< char > get_modelsel_names ()
void print_modsel_params ()
char * get_modsel_param_descr (const char *param_name)
index_t get_modsel_param_index (const char *param_name)
void build_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict)

Static Public Member Functions

static void * dense_dot_range_helper (void *p)
static SGVector< float64_tget_mean (CDotFeatures *lhs, CDotFeatures *rhs)
static SGMatrix< float64_tcompute_cov (CDotFeatures *lhs, CDotFeatures *rhs)

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
ParameterMapm_parameter_map
uint32_t m_hash

Protected Member Functions

void obtain_kmer_spectrum (CStringFeatures< uint16_t > *str)
void delete_kmer_spectrum ()
void display_progress (int32_t start, int32_t stop, int32_t v)
virtual TParametermigrate (DynArray< TParameter * > *param_base, const SGParamInfo *target)
virtual void one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)
virtual void load_serializable_pre () throw (ShogunException)
virtual void load_serializable_post () throw (ShogunException)
virtual void save_serializable_pre () throw (ShogunException)
virtual void save_serializable_post () throw (ShogunException)
virtual bool update_parameter_hash ()

Protected Attributes

bool use_normalization
int32_t num_strings
int32_t alphabet_size
int32_t spec_size
float64_t ** k_spectrum
float64_t combined_weight
 feature weighting in combined dot features
CSubsetStackm_subset_stack

Constructor & Destructor Documentation

default constructor

Definition at line 16 of file ExplicitSpecFeatures.cpp.

CExplicitSpecFeatures ( CStringFeatures< uint16_t > *  str,
bool  normalize = true 
)

constructor

Parameters:
str stringfeatures (of words)
normalize whether to use sqrtdiag normalization

Definition at line 30 of file ExplicitSpecFeatures.cpp.

copy constructor

Definition at line 43 of file ExplicitSpecFeatures.cpp.

~CExplicitSpecFeatures (  )  [virtual]

destructor

Definition at line 51 of file ExplicitSpecFeatures.cpp.


Member Function Documentation

int32_t add_preprocessor ( CPreprocessor p  )  [virtual, inherited]

set preprocessor

add preprocessor

Parameters:
p preprocessor to set
Returns:
something inty

Definition at line 81 of file Features.cpp.

void add_subset ( SGVector< index_t subset  )  [virtual, inherited]

adds a subset of indices on top of the current subsets (possibly subset o subset. Calls subset_changed_post() afterwards

Parameters:
subset subset of indices to add

Reimplemented in CCombinedFeatures.

Definition at line 351 of file Features.cpp.

void add_to_dense_vec ( float64_t  alpha,
int32_t  vec_idx1,
float64_t vec2,
int32_t  vec2_len,
bool  abs_val = false 
) [virtual]

add vector 1 multiplied with alpha to dense vector2

Parameters:
alpha scalar alpha
vec_idx1 index of first vector
vec2 pointer to real valued vector
vec2_len length of real valued vector
abs_val if true add the absolute value

Implements CDotFeatures.

Definition at line 89 of file ExplicitSpecFeatures.cpp.

void benchmark_add_to_dense_vector ( int32_t  repeats = 5  )  [inherited]

run benchmark for add_to_dense_vec

Definition at line 318 of file DotFeatures.cpp.

void benchmark_dense_dot_range ( int32_t  repeats = 5  )  [inherited]

run benchmark for dense_dot_range

Definition at line 341 of file DotFeatures.cpp.

void build_parameter_dictionary ( CMap< TParameter *, CSGObject * > &  dict  )  [inherited]

Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.

Parameters:
dict dictionary of parameters to be built.

Definition at line 1201 of file SGObject.cpp.

bool check_feature_compatibility ( CFeatures f  )  const [inherited]

check feature compatibility

Parameters:
f features to check for compatibility
Returns:
if features are compatible

Definition at line 326 of file Features.cpp.

void clean_preprocessors (  )  [inherited]

clears all preprocs

Definition at line 137 of file Features.cpp.

SGMatrix< float64_t > compute_cov ( CDotFeatures lhs,
CDotFeatures rhs 
) [static, inherited]

compute the covariance of two CDotFeatures together

Returns:
covariance

Definition at line 469 of file DotFeatures.cpp.

CFeatures * copy_subset ( SGVector< index_t indices  )  [virtual, inherited]

Creates a new CFeatures instance containing copies of the elements which are specified by the provided indices.

This method is needed for a KernelMachine to store its model data. NOT IMPLEMENTED!

Parameters:
indices indices of feature elements to copy
Returns:
new CFeatures instance with copies of feature data

Reimplemented in CCombinedFeatures, CDenseFeatures< ST >, CSparseFeatures< ST >, CStringFeatures< ST >, CDenseFeatures< uint32_t >, CDenseFeatures< float64_t >, CDenseFeatures< T >, CDenseFeatures< uint16_t >, CSparseFeatures< float64_t >, CSparseFeatures< T >, CStringFeatures< T >, CStringFeatures< uint8_t >, CStringFeatures< char >, and CStringFeatures< uint16_t >.

Definition at line 374 of file Features.cpp.

virtual CFeatures* create_merged_copy ( CFeatures other  )  [virtual, inherited]

Takes another feature instance and returns a new instance which is a concatenation of a copy if this instace's data and the given instance's data. Note that the feature types have to be equal.

NOT IMPLEMENTED!

Parameters:
other feature object to append
Returns:
new feature object which contains copy of data of this instance and of given one

Reimplemented in CCombinedFeatures, CDenseFeatures< ST >, CDenseFeatures< uint32_t >, CDenseFeatures< float64_t >, CDenseFeatures< T >, and CDenseFeatures< uint16_t >.

Definition at line 234 of file Features.h.

virtual CSGObject* deep_copy (  )  const [virtual, inherited]

A deep copy. All the instance variables will also be copied.

Definition at line 131 of file SGObject.h.

CPreprocessor * del_preprocessor ( int32_t  num  )  [virtual, inherited]

del current preprocessor

delete preprocessor from list caller has to clean up returned preproc

Parameters:
num index of preprocessor in list

Definition at line 143 of file Features.cpp.

void delete_kmer_spectrum (  )  [protected]

free kmer spectrum

Definition at line 139 of file ExplicitSpecFeatures.cpp.

float64_t dense_dot ( int32_t  vec_idx1,
const float64_t vec2,
int32_t  vec2_len 
) [virtual]

compute dot product between vector1 and a dense vector

Parameters:
vec_idx1 index of first vector
vec2 pointer to real valued vector
vec2_len length of real valued vector

Implements CDotFeatures.

Definition at line 76 of file ExplicitSpecFeatures.cpp.

void dense_dot_range ( float64_t output,
int32_t  start,
int32_t  stop,
float64_t alphas,
float64_t vec,
int32_t  dim,
float64_t  b 
) [virtual, inherited]

Compute the dot product for a range of vectors. This function makes use of dense_dot alphas[i] * sparse[i]^T * w + b

Parameters:
output result for the given vector range
start start vector range from this idx
stop stop vector range at this idx
alphas scalars to multiply with, may be NULL
vec dense vector to compute dot product with
dim length of the dense vector
b bias

note that the result will be written to output[0...(stop-start-1)]

Reimplemented in CCombinedDotFeatures, and CHashedWDFeaturesTransposed.

Definition at line 67 of file DotFeatures.cpp.

void * dense_dot_range_helper ( void *  p  )  [static, inherited]

Compute the dot product for a range of vectors. This function is called by the threads created in dense_dot_range

Reimplemented in CHashedWDFeaturesTransposed.

Definition at line 231 of file DotFeatures.cpp.

void dense_dot_range_subset ( int32_t *  sub_index,
int32_t  num,
float64_t output,
float64_t alphas,
float64_t vec,
int32_t  dim,
float64_t  b 
) [virtual, inherited]

Compute the dot product for a subset of vectors. This function makes use of dense_dot alphas[i] * sparse[i]^T * w + b

Parameters:
sub_index index for which to compute outputs
num length of index
output result for the given vector range
alphas scalars to multiply with, may be NULL
vec dense vector to compute dot product with
dim length of the dense vector
b bias

Reimplemented in CCombinedDotFeatures, and CHashedWDFeaturesTransposed.

Definition at line 153 of file DotFeatures.cpp.

float64_t dense_dot_sgvec ( int32_t  vec_idx1,
const SGVector< float64_t vec2 
) [virtual, inherited]

compute dot product between vector1 and a dense vector

Parameters:
vec_idx1 index of first vector
vec2 dense vector

Definition at line 62 of file DotFeatures.cpp.

void display_progress ( int32_t  start,
int32_t  stop,
int32_t  v 
) [protected, inherited]

display progress output

Parameters:
start minimum value
stop maximum value
v current value

Definition at line 528 of file DotFeatures.cpp.

float64_t dot ( int32_t  vec_idx1,
CDotFeatures df,
int32_t  vec_idx2 
) [virtual]

compute dot product between vector1 and vector2, appointed by their indices

Parameters:
vec_idx1 index of first vector
df DotFeatures (of same kind) to compute dot product with
vec_idx2 index of second vector

Implements CDotFeatures.

Definition at line 61 of file ExplicitSpecFeatures.cpp.

CFeatures * duplicate (  )  const [virtual]

duplicate feature object

Returns:
feature object

Implements CFeatures.

Definition at line 148 of file ExplicitSpecFeatures.cpp.

void free_feature_iterator ( void *  iterator  )  [virtual]

clean up iterator call this function with the iterator returned by get_first_feature

Parameters:
iterator as returned by get_first_feature

Implements CDotFeatures.

Definition at line 167 of file ExplicitSpecFeatures.cpp.

int32_t get_cache_size (  )  const [inherited]

get cache size

Returns:
cache size

Definition at line 203 of file Features.cpp.

float64_t get_combined_feature_weight (  )  [inherited]

get combined feature weight

Returns:
combined feature weight

Definition at line 151 of file DotFeatures.h.

SGMatrix< float64_t > get_computed_dot_feature_matrix (  )  [inherited]

compute the feature matrix in feature space

Returns:
computed feature matrix

Definition at line 284 of file DotFeatures.cpp.

SGVector< float64_t > get_computed_dot_feature_vector ( int32_t  num  )  [inherited]

compute the feature vector in feature space

Returns:
computed feature vector

Definition at line 305 of file DotFeatures.cpp.

SGMatrix< float64_t > get_cov (  )  [virtual, inherited]

get covariance

Returns:
covariance

Definition at line 427 of file DotFeatures.cpp.

int32_t get_dim_feature_space (  )  const [virtual]

obtain the dimensionality of the feature space

(not mix this up with the dimensionality of the input space, usually obtained via get_num_features())

Returns:
dimensionality

Implements CDotFeatures.

Definition at line 56 of file ExplicitSpecFeatures.cpp.

EFeatureClass get_feature_class (  )  const [virtual]

get feature class

Returns:
feature class

Implements CFeatures.

Definition at line 183 of file ExplicitSpecFeatures.cpp.

void * get_feature_iterator ( int32_t  vector_index  )  [virtual]

iterate over the non-zero features

call get_feature_iterator first, followed by get_next_feature and free_feature_iterator to cleanup

Parameters:
vector_index the index of the vector over whose components to iterate over
Returns:
feature iterator (to be passed to get_next_feature)

Implements CDotFeatures.

Definition at line 155 of file ExplicitSpecFeatures.cpp.

EFeatureType get_feature_type (  )  const [virtual]

get feature type

Returns:
templated feature type

Implements CFeatures.

Definition at line 178 of file ExplicitSpecFeatures.cpp.

SGIO * get_global_io (  )  [inherited]

get the io object

Returns:
io object

Definition at line 224 of file SGObject.cpp.

Parallel * get_global_parallel (  )  [inherited]

get the parallel object

Returns:
parallel object

Definition at line 259 of file SGObject.cpp.

Version * get_global_version (  )  [inherited]

get the version object

Returns:
version object

Definition at line 272 of file SGObject.cpp.

SGVector< float64_t > get_mean (  )  [virtual, inherited]

get mean

Returns:
mean returned

Definition at line 384 of file DotFeatures.cpp.

SGVector< float64_t > get_mean ( CDotFeatures lhs,
CDotFeatures rhs 
) [static, inherited]

get mean of two CDotFeature objects

Returns:
mean returned

Definition at line 402 of file DotFeatures.cpp.

SGStringList< char > get_modelsel_names (  )  [inherited]
Returns:
vector of names of all parameters which are registered for model selection

Definition at line 1108 of file SGObject.cpp.

char * get_modsel_param_descr ( const char *  param_name  )  [inherited]

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

Parameters:
param_name name of the parameter
Returns:
description of the parameter

Definition at line 1132 of file SGObject.cpp.

index_t get_modsel_param_index ( const char *  param_name  )  [inherited]

Returns index of model selection parameter with provided index

Parameters:
param_name name of model selection parameter
Returns:
index of model selection parameter with provided name, -1 if there is no such

Definition at line 1145 of file SGObject.cpp.

virtual const char* get_name (  )  const [virtual]
Returns:
object name

Implements CSGObject.

Definition at line 169 of file ExplicitSpecFeatures.h.

bool get_next_feature ( int32_t &  index,
float64_t value,
void *  iterator 
) [virtual]

iterate over the non-zero features

call this function with the iterator returned by get_first_feature and call free_feature_iterator to cleanup

Parameters:
index is returned by reference (-1 when not available)
value is returned by reference
iterator as returned by get_first_feature
Returns:
true if a new non-zero feature got returned

Implements CDotFeatures.

Definition at line 161 of file ExplicitSpecFeatures.cpp.

int32_t get_nnz_features_for_vector ( int32_t  num  )  [virtual]

get number of non-zero features in vector

Parameters:
num which vector
Returns:
number of non-zero features in vector

Implements CDotFeatures.

Definition at line 172 of file ExplicitSpecFeatures.cpp.

int32_t get_num_preprocessed (  )  const [inherited]

get whether specified preprocessor (or all if num=1) was/were already applied

get the number of applied preprocs

Returns:
number of applied preprocessors

Definition at line 123 of file Features.cpp.

int32_t get_num_preprocessors (  )  const [inherited]

get number of preprocessors

Returns:
number of preprocessors

Definition at line 198 of file Features.cpp.

int32_t get_num_vectors (  )  const [virtual]

get number of strings

Returns:
number of strings

Implements CFeatures.

Definition at line 188 of file ExplicitSpecFeatures.cpp.

CPreprocessor * get_preprocessor ( int32_t  num  )  const [inherited]

get current preprocessor

get specified preprocessor

Parameters:
num index of preprocessor in list

Definition at line 111 of file Features.cpp.

int32_t get_size (  )  const [virtual]

get size of one element

Returns:
size of one element

Implements CFeatures.

Definition at line 193 of file ExplicitSpecFeatures.cpp.

CSubsetStack * get_subset_stack (  )  [virtual, inherited]

returns subset stack

Returns:
subset stack

Definition at line 369 of file Features.cpp.

bool has_property ( EFeatureProperty  p  )  const [inherited]

check if features have given property

Parameters:
p feature property
Returns:
if features have given property

Definition at line 336 of file Features.cpp.

bool is_generic ( EPrimitiveType *  generic  )  const [virtual, inherited]

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

Parameters:
generic set to the type of the generic if returning TRUE
Returns:
TRUE if a class template.

Definition at line 278 of file SGObject.cpp.

bool is_preprocessed ( int32_t  num  )  const [inherited]

get whether specified preprocessor was already applied

Parameters:
num index of preprocessor in list

Definition at line 193 of file Features.cpp.

void list_feature_obj (  )  const [inherited]

list feature object

Definition at line 214 of file Features.cpp.

void load ( CFile loader  )  [virtual, inherited]
DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile file,
const char *  prefix = "" 
) [inherited]

maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)

Parameters:
file_version parameter version of the file
current_version version from which mapping begins (you want to use VERSION_PARAMETER for this in most cases)
file file to load from
prefix prefix for members
Returns:
(sorted) array of created TParameter instances with file data

Definition at line 679 of file SGObject.cpp.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo param_info,
int32_t  file_version,
CSerializableFile file,
const char *  prefix = "" 
) [inherited]

loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned

Parameters:
param_info information of parameter
file_version parameter version of the file, must be <= provided parameter version
file file to load from
prefix prefix for members
Returns:
new array with TParameter instances with the attached data

Definition at line 523 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
) [virtual, inherited]

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

Parameters:
file where to load from
prefix prefix for members
param_version (optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 354 of file SGObject.cpp.

void load_serializable_post (  )  throw (ShogunException) [protected, virtual, inherited]

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.

Exceptions:
ShogunException Will be thrown if an error occurres.

Reimplemented in CLinearHMM, CAlphabet, CANOVAKernel, CCircularKernel, CExponentialKernel, CGaussianKernel, CInverseMultiQuadricKernel, CKernel, CWeightedDegreePositionStringKernel, and CList.

Definition at line 1033 of file SGObject.cpp.

void load_serializable_pre (  )  throw (ShogunException) [protected, virtual, inherited]

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.

Exceptions:
ShogunException Will be thrown if an error occurres.

Definition at line 1028 of file SGObject.cpp.

void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
) [inherited]

Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match

Parameters:
param_base set of TParameter instances that are mapped to the provided target parameter infos
base_version version of the parameter base
target_param_infos set of SGParamInfo instances that specify the target parameter base

Definition at line 717 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
) [protected, virtual, inherited]

creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.

If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass

Parameters:
param_base set of TParameter instances to use for migration
target parameter info for the resulting TParameter
Returns:
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

Definition at line 923 of file SGObject.cpp.

void obtain_kmer_spectrum ( CStringFeatures< uint16_t > *  str  )  [protected]

obtain the k-spectrum from a list of strings

Parameters:
str the string feature object already in k-mer format

Definition at line 107 of file ExplicitSpecFeatures.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
) [protected, virtual, inherited]

This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)

Parameters:
param_base set of TParameter instances to use for migration
target parameter info for the resulting TParameter
replacement (used as output) here the TParameter instance which is returned by migration is created into
to_migrate the only source that is used for migration
old_name with this parameter, a name change may be specified

Definition at line 864 of file SGObject.cpp.

void print_modsel_params (  )  [inherited]

prints all parameter registered for model selection and their type

Definition at line 1084 of file SGObject.cpp.

void print_serializable ( const char *  prefix = ""  )  [virtual, inherited]

prints registered parameters out

Parameters:
prefix prefix for members

Definition at line 290 of file SGObject.cpp.

void remove_all_subsets (  )  [virtual, inherited]

removes all subsets Calls subset_changed_post() afterwards

Reimplemented in CCombinedFeatures.

Definition at line 363 of file Features.cpp.

void remove_subset (  )  [virtual, inherited]

removes that last added subset from subset stack, if existing Calls subset_changed_post() afterwards

Reimplemented in CCombinedFeatures.

Definition at line 357 of file Features.cpp.

bool reshape ( int32_t  num_features,
int32_t  num_vectors 
) [virtual, inherited]

in case there is a feature matrix allow for reshaping

NOT IMPLEMENTED!

Parameters:
num_features new number of features
num_vectors new number of vectors
Returns:
if reshaping was successful

Reimplemented in CDenseFeatures< ST >, CDenseFeatures< uint32_t >, CDenseFeatures< float64_t >, CDenseFeatures< T >, and CDenseFeatures< uint16_t >.

Definition at line 208 of file Features.cpp.

void save ( CFile writer  )  [virtual, inherited]
bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
) [virtual, inherited]

Save this object to file.

Parameters:
file where to save the object; will be closed during returning if PREFIX is an empty string.
prefix prefix for members
param_version (optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 296 of file SGObject.cpp.

void save_serializable_post (  )  throw (ShogunException) [protected, virtual, inherited]

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.

Exceptions:
ShogunException Will be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1043 of file SGObject.cpp.

void save_serializable_pre (  )  throw (ShogunException) [protected, virtual, inherited]

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.

Exceptions:
ShogunException Will be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1038 of file SGObject.cpp.

void set_combined_feature_weight ( float64_t  nw  )  [inherited]

set combined kernel weight

Parameters:
nw new combined feature weight

Definition at line 157 of file DotFeatures.h.

void set_generic< floatmax_t > (  )  [inherited]

set generic type to T

void set_global_io ( SGIO io  )  [inherited]

set the io object

Parameters:
io io object to use

Definition at line 217 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel  )  [inherited]

set the parallel object

Parameters:
parallel parallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version version  )  [inherited]

set the version object

Parameters:
version version object to use

Definition at line 265 of file SGObject.cpp.

void set_preprocessed ( int32_t  num  )  [inherited]

set applied flag for preprocessor

Parameters:
num index of preprocessor in list

Definition at line 188 of file Features.cpp.

void set_property ( EFeatureProperty  p  )  [inherited]

set property

Parameters:
p kernel property to set

Definition at line 341 of file Features.cpp.

virtual CSGObject* shallow_copy (  )  const [virtual, inherited]

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 122 of file SGObject.h.

virtual void subset_changed_post (  )  [virtual, inherited]

method may be overwritten to update things that depend on subset

Reimplemented in CStringFeatures< ST >, CStringFeatures< T >, CStringFeatures< uint8_t >, CStringFeatures< char >, and CStringFeatures< uint16_t >.

Definition at line 262 of file Features.h.

void unset_generic (  )  [inherited]

unset generic type

this has to be called in classes specializing a template class

Definition at line 285 of file SGObject.cpp.

void unset_property ( EFeatureProperty  p  )  [inherited]

unset property

Parameters:
p kernel property to unset

Definition at line 346 of file Features.cpp.

bool update_parameter_hash (  )  [protected, virtual, inherited]

Updates the hash of current parameter combination.

Returns:
bool if parameter combination has changed since last update.

Definition at line 237 of file SGObject.cpp.


Member Data Documentation

int32_t alphabet_size [protected]

size of alphabet

Definition at line 187 of file ExplicitSpecFeatures.h.

float64_t combined_weight [protected, inherited]

feature weighting in combined dot features

Definition at line 246 of file DotFeatures.h.

SGIO* io [inherited]

io

Definition at line 462 of file SGObject.h.

float64_t** k_spectrum [protected]

k-mer counts for all strings

Definition at line 192 of file ExplicitSpecFeatures.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 480 of file SGObject.h.

model selection parameters

Definition at line 474 of file SGObject.h.

map for different parameter versions

Definition at line 477 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 471 of file SGObject.h.

CSubsetStack* m_subset_stack [protected, inherited]

subset used for index transformations

Definition at line 296 of file Features.h.

int32_t num_strings [protected]

number of strings

Definition at line 185 of file ExplicitSpecFeatures.h.

Parallel* parallel [inherited]

parallel

Definition at line 465 of file SGObject.h.

int32_t spec_size [protected]

size of k-mer spectrum

Definition at line 190 of file ExplicitSpecFeatures.h.

bool use_normalization [protected]

use sqrtdiag normalization

Definition at line 183 of file ExplicitSpecFeatures.h.

Version* version [inherited]

version

Definition at line 468 of file SGObject.h.


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